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Active Simultaneous Localization and Mapping (SLAM) is the problem of planning and controlling the motion of a robot to build the most accurate and complete model of the surrounding environment. Since the first foundational work in active…
Spatially annotated single-cell datasets provide unprecedented opportunities to dissect cell-cell communication in development and disease. Heterotypic signaling includes interactions between different cell types and is well established in…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
Program SMART (Spectra and Model Atmospheres by Radiative Transfer) has been composed for modelling atmospheres and spectra of hot stars (O, B and A spectral classes) and studying different physical processes in them (Sapar & Poolam\"ae…
Computer-based modelling and simulation have become useful tools to facilitate humans to understand systems in different domains, such as physics, astrophysics, chemistry, biology, economics, engineering and social science. A complex system…
Signaling pathways serve to communicate information about extracellular conditions into the cell, to both the nucleus and cytoplasmic processes to control cell responses. Genetic mutations in signaling network components are frequently…
Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…
Epithelial-Mesenchymal Transition (EMT), and the corresponding reverse process, Mesenchymal-Epithelial Transition (MET), are dynamic and reversible cellular programs orchestrated by many changes at biochemical and morphological levels. A…
The user of Engineering Manuals (EM) finds it difficult to read EM s because they are long, have a dense format which includes written documents, step by step procedures, and standard parameter lists for engineering equipment. Off the shelf…
We propose spatially-adaptive normalization, a simple but effective layer for synthesizing photorealistic images given an input semantic layout. Previous methods directly feed the semantic layout as input to the deep network, which is then…
In multicellular organisms, cells coordinate their activities through cell-cell communication (CCC), which is crucial for development, tissue homeostasis, and disease progression. Recent advances in single-cell and spatial omics…
Biological neurons can detect complex spatio-temporal features in spiking patterns via their synapses spread across across their dendritic branches. This is achieved by modulating the efficacy of the individual synapses, and by exploiting…
We present a framework for simulating signal propagation in geometric networks (i.e. networks that can be mapped to geometric graphs in some space) and for developing algorithms that estimate (i.e. map) the state and functional topology of…
Recent studies have shown how spiking networks can learn complex functionality through error-correcting plasticity, but the resulting structures and dynamics remain poorly studied. To elucidate how these models may link to observed dynamics…
In biological cells and novel diagnostic devices biochemical receptors need to be sensitive to extremely small concentration changes of signaling molecules. The accuracy of such molecular signaling is ultimately limited by the counting…
Capturing the structure of a data-generating process by means of appropriate inductive biases can help in learning models that generalize well and are robust to changes in the input distribution. While methods that harness spatial and…
We present the MIM calculus, a modeling formalism with a strong biological basis, which provides biologically-meaningful operators for representing the interaction capabilities of molecular species. The operators of the calculus are…
A cell can be seen as an adaptive autonomous agent or as a society of adaptive autonomous agents, where each can exhibit a particular behaviour depending on its cognitive capabilities. We present an intracellular signalling model obtained…
Stochastic models of biochemical reaction networks are widely used to capture intrinsic noise in cellular systems. The typical formulation of these models are based on Markov processes for which there is extensive research on efficient…